Chemistry 20 Chapter 14 Proteins

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1 Chapter 14 Proteins Proteins: all proteins in humans are polymers made up from 20 different amino acids. Proteins provide structure in membranes, build cartilage, muscles, hair, nails, and connective tissue (wool, silk, feathers, and horns are some other proteins made by animals), transport oxygen in blood and muscle, direct biological reactions as enzymes, defend the body against infection, and control metabolic processes as hormones. They can even be a source of energy. Different functions of proteins depend on the structure and chemical behavior of amino acids, the building blocks of proteins. Amino acids: proteins are composed of molecular building blocks called amino acids. An amino acid contains two functional groups, an amino group (-NH2) and a carboxylic acid group (-CH). In all of the 20 amino acids found in proteins, the amino group, the carboxylic group, and a hydrogen atom are bonded to a central carbon atom. Amino acids with this structure are called α (alpha) amino acids. Although there are many amino acids, only 20 different amino acids are present in the proteins in humans. The unique characteristics of the 20 amino acids are due to a side chain (-), which can be an alkyl, hydroxyl, thiol, amino, sulphide, aromatic, or cyclic group. Dr. Behrang Madani Mt SAC

2 Zwitterion: although it is convenient to write amino acids with carboxyl (-CH) group and amino (-NH2) group, they are usually ionized. At the ph of most body fluids, the carboxyl group loses a H, giving C-, and the amino group accepts a H to give an ammonium ion, -NH3. The dipolar form of an amino acid, called a Zwitterion, has a net charge of zero (it is neutral). Classification of Amino acids: 1. Nonpolar amino acids: which have alkyl or aromatic side chains, are hydrophobic ( water-fearing ). 2. Polar amino acids: which have polar side chains such as hydroxyl (-H), thiol (-SH), and amide (-CNH2) that form hydrogen bonds with water, are hydrophilic ( water attracting ). 3. Acidic amino acids: have side chains that contain a carboxylic group (-CH) and can ionize as a weak acid. 4. Basic amino acids: have side chains that contain an amino group that can ionize as a weak base. D and L isomer: all of the α-amino acids (except for glycine) are chiral because the α carbon is attached to four different atoms. Thus amino acids can exist as D and L isomers (enantiomers). For the L isomer the amino group, NH2, is on the left, and in the D isomer, it is on the right. In biological systems, only L amino acids are incorporated into proteins. There are D amino acids found in nature, but not in proteins. Ionization and ph: at a certain ph known as the isoelectric point (pi), the positive and negative charges are equal, which gives an overall charge of zero (no net charge). The zwitterions for polar and nonpolar amino acids typically exist at ph values of 5.0 to 6.0. However, in a solution that is more acidic than the pi (ph about 2 or 3), the C- group acts as a base and accepts an H, which gives an overall positive charge to the amino acid (net charge 1): H3 N-CH-C- H3 H3 N-CH-C-H H2 In a solution more basic than the pi (ph from 7.6 to 10.8), the NH3 group acts as an acid and loses an H, which gives the amino acid an overall negative charge (net charge 1): H3 N-CH-C- H Dr. Behrang Madani H2 N-CH-C- H2 Mt SAC

3 As a result, the net charge on an amino acid depends on the ph of the solution in which it is dissolved. Each amino acid has a constant pi (isoelectric point) and by comparison of values of pi and ph of solution, we can find the charge of an amino acid. H - H 3 N-CH-C- - H - H 3 N-CH-C-H H 2 N-CH-C- - H H 3 3 ph 2.0 ph ph 10.0 Net charge 1 Net charge 0 N et ch arge -1 Peptide: the linking of two or more amino acids forms a peptide. A peptide bond is an amide bond that forms when the C - group of one amino acid reacts with the NH 3 group of the next amino acid. Note: Two amino acids linked together by a peptide bond form a dipeptide, three amino acids from tripeptide, many amino acids form polypeptide. Protein is a biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds. peptide bond CH 3 H 3 N Alanine (Ala) - H 3 N - CH 2 H Serine (Ser) H 3 N CH 3 H N - CH 2 H Alanylserine (Ala-Ser) H 2 Note: In a peptide, the amino acid written on the left with the unreacted or free amino group (-NH 3 ) is called the N terminal amino acid. The C terminal amino acid is the last amino acid in the chain with the unreacted or free carboxyl group (-C - ). Naming of peptide: in naming a peptide, each amino acid beginning from the N terminal is named with a -yl ending (we drop the -ine and we replace -yl ) followed by the full name of the amino acid at the C terminal. For example, a tripeptide consisting of alanine, glycine, and serine is named as alanylglycylserine. For convenience, the order of amino acids in the peptide is often written as the sequence of three-letter abbreviations. Dr. Behrang Madani Mt SAC

4 Levels of protein structure: Each protein in our cells has a unique sequence of amino acids that determines in biological function. Four levels exist for structure of the proteins: 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure 1. Primary Structure: The primary structure is the order of the amino acids held together by peptide bonds. The first protein to have its primary structure determined was insulin, which is a hormone that regulated the glucose level in the blood. In the primary structure of human insulin, there are two polypeptide chains. In the chain A, there are 21 amino acids, and chain B has 30 amino acids. The polypeptide chains are held together by disulfide bonds formed by the side chains of the cysteine amino acids in each of the chains. Today human insulin produced through genetic engineering is used in the treatment of diabetes. Note: The -SH (sulfhydryl) group of cysteine (an amino acid) is easily oxidized to an -S-S(disulfide). 2 H3 N-CH-CCH2 SH Cysteine oxidation reduction H3 N-CH-C CH2 a disulfide bon d S S CH 2 H3 N-CH-C Cystine Secondary structure: the secondary structure of a protein describes the way the amino acids next to or near to each other along the polypeptide are arranged in space. The three most common types of secondary structure are the alpha helix, the beta-pleated sheet, and the triple helix found in collagen. Alpha helix (α-helix): the corkscrew shape of an alpha helix is held in place by hydrogen bonds between each N-H group and the oxygen of a C= group in the next turn of the helix, four amino acids down the chain. Because many hydrogen bonds form along the peptide backbone, this portion of the protein takes the shape of a strong, tight coil that looks a Dr. Behrang Madani Mt SAC

5 telephone cord or a Slinky toy. All the side chains ( groups) of the amino acids are located on the outside of the helix. H-bond Beta-pleated sheet (β-pleated sheet): in a β-pleated sheet, polypeptide chains are held together side by side by hydrogen bonds between the peptide chains. In a β-pleated sheet of silk fibroin, the small groups of the prevalent amino acids, glycine, alanine, and serine, extend above and below the sheet. This result in a series of β-pleated sheets that are stacked close together. The hydrogen bonds holding the β-pleated sheets tightly in place account for the strength and durability of proteins such as silk. H Triple helix (Collagen): the most abundant protein, makes up as one-third of all the protein in vertebrates. It is found in connective tissue, blood vessels, skin, tendons, ligaments, the cornea of the eye, and cartilage. The strong structure of collagen is a result of three polypeptides woven together like a braid to form a triple helix. Collagen has a high content of glycine (33%), praline (22%), alanine (12%), and smaller amounts of hydroxyproline, and hdroxylysine. The hydroxyl forms of praline and lysine contain H groups that form hydrogen bonds across the peptide chains and give strength to the collagen triple helix. Note: When a diet is deficient in vitamin C, collagen fibrils are weakened because the enzymes needed to form hydoxyproline and hydroxylysine require vitamin C. Without the Dr. Behrang Madani Mt SAC

6 H groups of hydroxyproline and hydroxylysine, there is less hydrogen bonding between collagen fibrils. As a person ages, additional cross-links form between the fibrils, which make collagen less elastic. Bones, cartilage, and tendons become more brittle, and wrinkles are seen as the skin loses elasticity. Tertiary structure: the tertiary structure of a protein involves attractions and repulsions between the side chain groups of the amino acids in the polypeptide chain. As interactions occur between different parts of the peptide chain, segments of the chain twist and bend until the protein acquires a specific three-dimensional shape. The tertiary structure of a protein is stabilized by interactions between the groups of the amino acids in one region of the polypeptide chain with groups of amino acids in other regions of the protein. There are five important interactions: 1. Hydrogen bond: occurs between H and or N. 2. Hydrophobic interactions: are interactions between two nonpolar groups. Within the protein, the amino acids with nonpolar side chains push as far away from the aqueous environment as possible, which forms a hydrophobic center at the interior of the molecule. 3. Hydrophilic interactions: are attractions between the external aqueous environment and amino acids that have polar or ionized side chains. The polar side chains pull toward the outer surface of globular proteins to hydrogen bond with water. 4. Salt bridges: are ionic bonds between side chains of basic and acidic amino acids, which have positive and negative charges. The attraction of the oppositely charged side chains forms a strong bond called a salt bridge. If the ph changes, the basic and acidic side chains lose their ionic charges and cannot form salt bridge, which causes a change in the shape of the protein. 5. Disulfide bonds: are the strong covalent links between sulfur atoms of two cysteine amino acids. Classification of proteins: 1-Globular proteins: a group of proteins known as globular proteins have compact, spherical shapes because sections of the polypeptide chain fold over on top of each other. It is the globular proteins that carry out the work of the cells: functions Dr. Behrang Madani Mt SAC

7 such as synthesis, transport, and metabolism. Myoglobin is a globular protein that stores oxygen in skeletal muscle. High concentrations of myoglobin are found in the muscles of sea mammals, such as seals and whales, which allow them to stay under the water for long periods. Myoglobin contains 153 amino acids in a single polypeptide chain with about threefourths of the chain in the α-helix secondary structure. Within the tertiary structure, a pocket of amino acids and a heme group binds and store oxygen. 2-Fibrous proteins: are proteins that consist of long, thin, fiber-like shapes. They are typically involved in the structure of cells and tissue. Two types of fibrous protein are α- and β-keratins. The α-keratins are the proteins that make up hair, wool, skin, and nails. In hair, three α-helixes coil together like a braid to form a fibril. Within the fibril, the α-helices are held together by disulfide (-S-S-) linkages between the groups of the many cysteine amino acids in hair. The β-keratins are the type of proteins found in the feathers of birds and scales of reptiles. In β-keratins, the proteins consist of large amount of β-pleated sheet structure. Quaternary structure: when a biologically active protein consists of two or more polypeptide subunits, the structure level is referred to as a quaternary structure. Hemoglobin, a globular protein that transports oxygen in blood, consists of four polypeptide chains or subunits, two α chains, and two β chains. The subunits are held together in the quaternary by the same interactions that stabilized the tertiary structure, such as hydrogen bonds and salt bridges between side groups, disulfide links, and hydrophobic attractions. Each subunit of the hemoglobin contains a heme group that binds oxygen. In the adult hemoglobin molecule, all four subunits must be combined for the hemoglobin to properly function as an oxygen carrier. Therefore, the complete quaternary structure of hemoglobin can bind and transport four molecules of oxygen. α chain β chain β chain α chain Summary of structural level in proteins: Dr. Behrang Madani Mt SAC

8 Denaturation of proteins: denaturation of a protein occurs when there is a disruption of any of the bonds that stabilize the secondary, tertiary, or quaternary structure. However, the covalent amide bonds of the primary structure are not affected. When the interactions between the groups are undone or altered, a globular protein unfolds like a piece of spaghetti. With the loss of its overall shape, the protein is no longer biologically active. Denaturation agents include heat, acids and bases, organic compounds, heavy metal ions, and mechanical agitation. The following table shows some examples of proteins denaturation. Some denaturatins are reversible, while others permanently damage the protein. For example, heat cleaves hydrogen bonds, so boiling a protein solution destroys the α-helical and β-pleated sheet structure. Alcohols denature hydrogen bonds and hydrophilic interactions in proteins. This process is used in sterilizing the skin before injection (to kill bacteria). Heavy metals ions (Pb2, Hg2, and Cd2) also denature proteins by attacking the SH groups. They form salt bridges, as in SHg2-S- Dr. Behrang Madani Mt SAC

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